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Now you've got the same effect: when creating or editing entries in the admin, you'll only see the field which accepts Markdown syntax (body_markdown), but when saving, the "body" field will be auto-filled with the corresponding XHTML. Then in your template, you can pull in entry.body, and save yourself a little processing time everytime the page is loaded.

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Also it's gonna be more efficient to have a Markdown Field that do the job, below you can see some snippets and code example about how to implement such a field.